My interpretation of this song is that the song is from the perspective of the many and how they relate/react to this "cruel world".
"You are mine and we are twine" and "When we radiate in wave together everything is fine" Indicate how we are connected to the world and when we work together with the earth things are okay. Unfortunately this is not the case in the current world.
To me the chorus represents how many of us recognize that the world is killing us but we still do not do much but ask for sympathy and are "as blind as a fool can be". I think the last line is how the world we have made does not think about the common man.
The second verse is to me about how many feel alone and isolated with how the world is not but we still turn to this world things from it for comfort.
small things: This cruel world is our everything and we have made a mess of everything.
the two people narrative works to but just doesn't sit well with me.

It could be any religion though really (or a belief system that acts as a religion)

It's honestly kind of straightforward and I'm surprised I haven't seen anyone suggest this. (Sorry if someone did suggest it I just didn't see it 😂)

The dudes an atheist and he's dating a Christian and he's having internal moral conflict about their relationships and differing points of view.

the line "When we radiate in waves together, everything is fine", to me, implies that though he faces moral conflict, the song's 'protagonist' forgets his objections when they have sex.

I think this song holds parallel meanings:

• On a personal level, it could be, as the above-poster (Brendan) said, about a loved-one who can't let go of their superstitions, but is nevertheless loved by the author.

On a global level, this is probably about the author's love of the world and humanity within it, despite the huge gaping flaw in humanity of (again) clinging to superstitious, unreasoning modes of thinking. The world can be a cruel place, and a big part of that cruelty stems from, or is enhanced by dogmatic thinking. Nevertheless, the author bears no hatred for the world, and, in fact loves humanity, despite (and maybe even sometimes because of) its flaws.

This is my favorite song on the album. As I reflect on it, I'm leaning towards wanting to believe that the song is simply a story about (the narrator) a person who cannot penetrate through the beliefs of another. Maybe Mr. Brett has a religious loved one that won't even hear his point of view?

"But I can penetrate your religion with a nail"

sounds like an allusion to the crucifications during the Roman Empire to me